Download Chapter 17 Notes : From Gene to Protien

Chapter 17 Notes : From Gene to Protien
Archibald Gerrod-1909
Was the first scientist to suggest that genes dictate phenotypes through enzymes->
symptoms of an inherrited disease come from incapability to create a certain enzyme.
Ex.Alkaptonuria-black pee because those with it are incapable of making the enzyme that
breaks alkapton down.
How Genes Control Metabolism-1 Gene, 1 Enzyme
Cells degrade and synthesize organic molecules through metabolic
pathways.Each reaction in these sequences is catalyzed by a specific enzyme.
Ex. In fruit flies’ eye color, mutations block pigment synthesis at a specific step of
a pathway by preventing an enzyme corresponding to that step. (Beadle and Ephrussi)
Beadle and Tatum worked with Neurospora crassa by exposing them to X rays
and then locating mutants. The wild type have minimal requirements-surviving on agar,
salt, glucose, and boitin. Mutants couldn’t survive on this, but were found to be able to
survive when supplied full medium-20 amino acids + other molecules.
The different classes of mutants were put into vials each containing the minimal +
1 additional supplement, so the supplement that allowed growth in the mutant would
show the defect.
Using genetic crosses, they found 3 classes of argenine-requiring mutants. The
argenine pathway : nutrient-> organine->citrulline->argenine. They tested each class for
different growth requirements, and found that each mutant lacks an enzyme that catalyzes
production of a specific chemical in the pathway.
This work provided evidence for 1 gene 1 enzyme-function of gene dictates
production of enzyme.
1 gene-1polypeptide
Not all protiens are enzymes, causing people to think 1 gene-1 protein. However
proteins are made from multiple polypeptide chains, each with its own gene. So… -> 1
gene, 1 polypeptide.
Gene to phenotype= DNA->RNA->Protein. RNA has ribose sugar and CAGU
bases, they’re usually 1 strand.
Synthesis of RNA by DNA’s direction=transcription.The RNA created form a
DNA strand is called mRNA because it carries genetic info to the protien synthesizing
machinery of the cell.
Translation is the production of a polypeptide under instruction of RNA-occurs on
robosomes. In prokaryotes, since DNA is free in the cytoplasm, nothing seperates it from
the robosomes, so transcription and translation are coupled. In eukaryotic cells, the
nucleus separates DNA from ribosomes, and mRNA is modified before leaving the
nucleus (pre-mRNA->RNA processing-> primary transcript.)
Since 4 nucleotides specify 20 amino acids, multiple nucleotides in sequences
must code for an amino acid. 3 nucleotides=1 codon=(codes for) 1 amino acid*.This is
called triplet code.
For each gene, only 1 strand (template strand) of the double helix is transcribed
into mRNA. NOTE : the template strand can alternate among each in the double helixpart of the template can be on 1 strand, and the other part on the other strand.
Cracking the Genetic Code
Nirenberg synthesized fake nRNA in a continuous UUUU sequence and added it
to amino acids, ribosomes, etc for protein synth and found that a long phenylalenine
(Phe) strand was made. Thus, UUU=phenylalenine. Similarexperiments took place for
other sequences.
Three of the codons are « stop » signals.
There is redundancy, but no ambiguity= 2 codons can code for the same thing, but
a codon cannot code for 2 different things.
The reading frame is important because it ensures that the sequence is being read
in the proper sequence of codons Ex. AAT UUG A, not A ATU UGA.
The genetic code is nearly universal, suggestive of a common ancestor. An
applcation : DNA of 1 species can be programmed by insertion of foreign DNA into
another to genetically modify a species.
RNA polymerase pries the 2 DNA strands apart and attaches RNA
nucleotides in 5 to 3 direction.
Promoter=sequence that signals beginning of transcription-upstream.
Terminator=signals end-downstream. Transcription unit : streach of DNA copied into
mRNA.
Prokaryotes have 1 kind of RNA polymerase, Eukaryotes have 3, I, II, and III. II
is used in mRNA synth.
3 Steps of transcription :
 Initiation
 Elongation
 Termination
Promoter also indicates which strand is template.
In prokaryotes :
RNA polymerase automatically binds to promoter region and begins working
In eukaryotes :
Transcription factors bind to the promoter region to create a transcription
initiation complex. The TATA box hepls recognize the promoter sequence and the
complementary strand, ATAT, is the one that is transcribed.
Elongation :
 RNA polymerase moves down the DNA strand unzipping it and adding
appropriate complementary RNA nucleotides
 The DNA strands reform and the RNA is peeled away after it at 60
nucleotides per second.
 A single strand can be transcribed multiple copies at a time becuase multiple
RNA polymerases bind to the strand and add nucleotides in a growing strand
that trails off from the polymerase.
Termination :
 Polymerase transcribes a terminator sequence in DNA. The RNA sequence is
what is the termination signal.
 In a prokaryotic cell, transcription ends right when this signal is found. In a
eukaryotic cell, it continues 100s of nucleotides after the sequence and then 1035 nucleotides after the stop sequence, the pre-mRNA is cut away from the
enzyme.
Alteration of mRNA ends.

The 5 end is capped with a modified G, which helps prevent degredation by
hydrolytic enzymes, and signals as an attachment spot for ribosomes.
 At the 3 end, a polytail A is added (repetitive AAA sequence 50-250 nucleotides
long.) It serves the same functions as the G cap, but also helps export mRNA
from the nucleus.
RNA cut and paste= RNA splicing.
Introns are cut away from exons, with the exception of the leader and trailer ends that
are introns.
 Short nucleotide sequences at the end of introns signal RNA splicing.
 Small nuclear ribonuclearprotiens recognize the slice sites. Many of these +
other proteins make a spilceosome.-cuts at points in the transcript to release
the intron and joins the 2 exons.
 Evidence shows that snRNA is catalytic-comes from discovery of ribozymesRNA that works as an enzyme.
 Ribozymes catalyze their own excision of introns
 Introns are said to play regulatory roles in the cell.
Alternative RNA splicing is what makes the variety of different enzymes in
organisms produced out of a limited RNA sequence. It is the variation of which
segments are treated as introns in processing.
Split genes also help evolution of new proteins. Proteins also have discrete
structural regions called domains. Usually, the different exons code for different
domains of a protien.
Introns increase probability of crossing over in genes by providing more
places where crossing over can occur.
Exon shuffling (moving to different chromosomes) can lead to new proteins.
It moves the correct amino acid from the sytoplasm into the ribosome as coded by
mRNA. The ribosome adds them to the chain.
 Each tRNA is different because it has the correct amino acid and the
anticodon at the other end, which complements a codon on the mRNA.
TRNA
 Transcribed from DNA & in eukaryotes is made in nucleus
 In both kinds of cells, each tRNA is reusedand recycled
 Its 1 strand of RNA 80 nucleotides long. It is in complex conformation
held together by hydrogen bonds. It looks like a clover leaf when
flattened.in form, it is L shaped, 1 branch having the antcodon, the other
with the amino acid, so structure fits function.
 Some tRNAs have anticodons that can recognize 2 of more different
codons because base pairing rules are not as strict, although it still must be
pyrimadine to purine. This relaxation is called a wobble. Wobbles are
what makes possible the variability in the genetic code (only in the case of
a wobble at the 3rd base). Iosine wobbles creat most versitality-can bond
with U C or A
BUT FIRST :
A tRNA must be paired with its amino acid.
Aminoacyl-tRNA synthetase= enzyme that binds tRNA to proper amino
acid. 20 of these in cell, 1 for each amino acid. Active site of 1 fits only 1
combination of tRNA and amino acid and attaches them by hydorlysis of
ATP.
Ribosomes :
 Have 2 subunits-larger and smaller
 Made of proteins and r RNA
 In eukaryotes, subunits are made in nucleolus-ribosomal genes are
transcribes from DNA and RNA is processed and assmbles with
proteins from the cytoplasm. The units are then exportes via nuclear
pores into cytopalsm
 2/3 a riosome is rRNA, and since ribosomes are most common in cells,
rRNA is the most abundant sort
 eukaryotic ribosomes are bigger and slightly chemically different, so
medicines can be used to affect ribosomes only of bacterial cells
 each has a P site for transfer RNA carrying growing amino acid train
and an A site for temporary attachment o tRNA as it delivers the
amino acids. Discharged t RNAs leave from E site.
 The ribosome holds the mRNA and tRNA close and positions the
amino acid on the polypeptide chain, adn then catalyzes peptide bond
 Most of tis proteins are on outside
Translation in 3 stages :
 Initiation
 Elongation
 Termination
NRG is provided to some of these phases through GTP
Initiation : brings together mRNA, a tRNA with the first amin acid,
and the 2 subunits of the ribosome.
1. small subunit binds to mRNA (at 5 end) and initiator tRNA
2. small ribosomal unit attaches to the leader strand upstream (5
prime) how this is done :
in prokaryotes, the leader strand attaches directly to
the small ribosomal subunit through base pairing. In
eukaryotes, the 5 prime cap signals the ribosome to
attach. Downstream from this, there is the inititation
codon which specifies to begin translation.
Sequence AUG-methionine
 the translation initiation complex formation is included
in initiation. ** it’s initiation factors that bring all these
things together-spends GTP.
 Following these events, the initiator tRNA moves to the
P site and the A site is now succeptible to a new tRNA.
Elongation :
 Addition of additional amino acids-requires elongation factors
Occurs in 3 steps :
1. codon recognition : hydrogen bonds between codon in A site and
anticodon on appropriate tRNA. Elongation factor is what moves
the tRNA to this site.-** requires 2 GTPs
2. peptide bond formation : rRNA of >subunit catalyzes the new
amino acid’s bondage to the polypeptide chain extending from the
P site. The chain jumps tRNA molecules to the one in the A site.
3. translocation : reguires 1 GTP tRNA in A site then moves to P site
–anticodons are still bonded to mRNA codon, moving it along too,
bringing the next codon to be available for translation. tRNA from
P site ismoved to E site and then exits.
Termination :
Stop codon is reached at A site : UAA, UAG, UGA and a release factor binds to it which
then adds a water molecule rather than an amino acid to the polypeptide chain. This rxn
hydrolyzes the bond that holds the polypeptide chain to the tRNA, freeing both. The
translation assembly deconstructs.
Polyribosomes :
Often, multiple ribosomes will stranlate the same mRNA strand. Theses strings of
ribosomes are called polyribosomes. Found in both kinds ofe cells.
A gene determines protien’s composition, and therefore it’s comformation and structure.
Oftentimes, in order to achieve the highest organization (structurally), a chaperonin
protien is necessary.
 Posttranslational modifications are sometimes required before the protien
can begin working in the cell.(attach :sugars, lipids, PO4 groups, etc)
 Could be cut and then rejoined differently with disulfide bridges, or could
be sttached to other proteins to make a complex.
There are 2 kinds o ribosomes & they can switch from one to other. If polypeptide chain
signals to ribosome to attach to ER it will.
: free
 Suspended in cytosol, synth proteins 4 cytosol
Bound :
 Attached 2 rough endoplasmic reticulum-proteins for endomembrane system +
secretion
ENDOMEMBRANE PROTEINS HAVE SIGNAL PEPTIDE-targets protien to ER
 A signal recognition particle recognizes this 20 bp sequence while it’sbeing
transcribed and adapts ribosome attachment to the ER. Elongation continues there
and the polypeptide chain enters the cisternal space via protien pore. Signal
peptide is removed and if the protein is to be secretary, it is released into the
solution in the cisternal space and if it is to be a membrane protein, it stays
partially embedded in the ER.
 Other kinds of signal peptides target polypeptides to other organelles. In these
cases, translation is completed in cytosol before it is exported to any of these.
RNA cen serve so many functions :
Catalytic, structural, informational.
The reason being that it can H bond to other nucleic acids, and create a
conformational shape with H bonds
Protein synthesis
Prokaryotes

Different
polymerases
 Transcription
MM
termination-stops
at stoip codon and
is cut
 Ribosomes are
different
 Simultaneous
transcription and
translation
Eukaryotes






Different polymerases
that depend on
transcription factors
Termination exceeds
stop codon and is cut
35-100 base pairs past it
Ribosomes are different
Independant
transcription and
translation-separated by
nucleus
RNA processing
Complicated
mechanisms for
targeting a protein to an
organelle
Mutations



Changes in DNA
Point mutations-alterations in 1 bp of a gene
If occurs in gamete or cell that produces offspring, the mutation can be
passed on.
 Hemoglobin mutation-sickle cell aneomia – homozygous recessive for it.
 2 classes of point mutations : base pair substitutions, and
insertions/deletions
silent mutations-base pair substitution that produces no affect on
the protein due to repetitions in the genetic code. Others will have
had little affect on the protein. However, it COULD seriously alter
the proteins conformation and structure and function. This could
be beneficial, or disruptive.
 Substitutions are usually missense mutations-codon still codes for amino
acid, but not necessarily the right one.
 Nonsence mutations-If a codon is mutated to a stop codon, the protien
will stop translating prematurely and will be shorter & prob dysfuntional.
Insertions and deletions :
 Additions or losses of nucleotide pairs
 Worse affects
 Will generally alter the reading phrame-frameshift mutations, unless
they occur in multiples of 3.
Mutagens

Errors in replication, repair, or recombination can cause mutations.
(spontaneous mutations)
 What causes these disruptions ? – mutagens like X rays,
 Mutagenic radiation : UV light etc…
 Chemical mutagens : base analouges- similar to nitrogenous bases, but
pair incorrectly in replication. Others insert themselves, distorting the
double helix. Others cause changes in the bases that change their pairing
properties
 Chemicals are screened to see if they produce these affects to see if they
are carcenogenic
A gene is a region of DNA whose product is either a polypeptide or an
RNA molecule.